Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/igor-1.4.0+dfsg/igor_src/Aligner.h
Examining data/igor-1.4.0+dfsg/igor_src/Bestscenarioscounter.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Bestscenarioscounter.h
Examining data/igor-1.4.0+dfsg/igor_src/CDR3SeqData.cpp
Examining data/igor-1.4.0+dfsg/igor_src/CDR3SeqData.h
Examining data/igor-1.4.0+dfsg/igor_src/Counter.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Counter.h
Examining data/igor-1.4.0+dfsg/igor_src/Coverageerrcounter.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Coverageerrcounter.h
Examining data/igor-1.4.0+dfsg/igor_src/Deletion.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Deletion.h
Examining data/igor-1.4.0+dfsg/igor_src/Dinuclmarkov.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Dinuclmarkov.h
Examining data/igor-1.4.0+dfsg/igor_src/Errorrate.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Errorrate.h
Examining data/igor-1.4.0+dfsg/igor_src/Errorscounter.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Errorscounter.h
Examining data/igor-1.4.0+dfsg/igor_src/ExtractFeatures.h
Examining data/igor-1.4.0+dfsg/igor_src/GenModel.cpp
Examining data/igor-1.4.0+dfsg/igor_src/GenModel.h
Examining data/igor-1.4.0+dfsg/igor_src/Genechoice.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Genechoice.h
Examining data/igor-1.4.0+dfsg/igor_src/HypermutationfullNmererrorrate.cpp
Examining data/igor-1.4.0+dfsg/igor_src/HypermutationfullNmererrorrate.h
Examining data/igor-1.4.0+dfsg/igor_src/Hypermutationglobalerrorrate.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Hypermutationglobalerrorrate.h
Examining data/igor-1.4.0+dfsg/igor_src/Insertion.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Insertion.h
Examining data/igor-1.4.0+dfsg/igor_src/IntStr.cpp
Examining data/igor-1.4.0+dfsg/igor_src/IntStr.h
Examining data/igor-1.4.0+dfsg/igor_src/Model_Parms.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Model_Parms.h
Examining data/igor-1.4.0+dfsg/igor_src/Model_marginals.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Model_marginals.h
Examining data/igor-1.4.0+dfsg/igor_src/Pgencounter.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Pgencounter.h
Examining data/igor-1.4.0+dfsg/igor_src/Rec_Event.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Rec_Event.h
Examining data/igor-1.4.0+dfsg/igor_src/Singleerrorrate.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Singleerrorrate.h
Examining data/igor-1.4.0+dfsg/igor_src/Utils.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Utils.h
Examining data/igor-1.4.0+dfsg/igor_src/main.cpp
Examining data/igor-1.4.0+dfsg/igor_src/Aligner.cpp
Examining data/igor-1.4.0+dfsg/igor_src/ExtractFeatures.cpp

FINAL RESULTS:

data/igor-1.4.0+dfsg/igor_src/main.cpp:257:4:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
			system(&("man igor")[0]);
data/igor-1.4.0+dfsg/igor_src/main.cpp:1565:3:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
		system(&("mkdir " + cl_path )[0]);
data/igor-1.4.0+dfsg/igor_src/main.cpp:1716:3:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
		system(&("mkdir " + cl_path + "run_demo")[0]);
data/igor-1.4.0+dfsg/igor_src/main.cpp:1750:4:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
			system(&("mkdir " + cl_path + "aligns")[0]);
data/igor-1.4.0+dfsg/igor_src/main.cpp:2058:4:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
			system(&("mkdir " + cl_path +  batchname + "output")[0]);
data/igor-1.4.0+dfsg/igor_src/main.cpp:2062:5:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
				system(&("mkdir " + cl_path +  batchname + "inference")[0]);
data/igor-1.4.0+dfsg/igor_src/main.cpp:2068:5:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
				system(&("mkdir " + cl_path +  batchname + "evaluate")[0]);
data/igor-1.4.0+dfsg/igor_src/main.cpp:2078:4:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
			system(&("mkdir " + cl_path +  batchname + "generated")[0]);
data/igor-1.4.0+dfsg/igor_src/Bestscenarioscounter.cpp:134:35:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		this->output_scenario_file_ptr->open(path_to_file + "best_scenarios_counts.csv");
data/igor-1.4.0+dfsg/igor_src/Coverageerrcounter.cpp:90:37:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			this->output_cov_err_v_file_ptr->open(path_to_file + "V_genes_cov_and_err.csv");
data/igor-1.4.0+dfsg/igor_src/Coverageerrcounter.cpp:103:37:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			this->output_cov_err_d_file_ptr->open(path_to_file + "D_genes_cov_and_err.csv");
data/igor-1.4.0+dfsg/igor_src/Coverageerrcounter.cpp:116:37:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			this->output_cov_err_j_file_ptr->open(path_to_file + "J_genes_cov_and_err.csv");
data/igor-1.4.0+dfsg/igor_src/Errorscounter.cpp:143:43:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			this->output_scenario_errors_file_ptr->open(path_to_file + "scenarios_background_and_errors.csv");
data/igor-1.4.0+dfsg/igor_src/Errorscounter.cpp:150:51:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		this->output_sequence_averaged_errors_file_ptr->open(path_to_file + "sequence_mutation_frequency.csv");
data/igor-1.4.0+dfsg/igor_src/GenModel.cpp:501:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		outfile_ind_seq.open(filename_ind_seq);
data/igor-1.4.0+dfsg/igor_src/GenModel.cpp:502:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		outfile_ind_real.open(filename_ind_real);
data/igor-1.4.0+dfsg/igor_src/HypermutationfullNmererrorrate.cpp:173:27:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	output_Nmer_stat_stream->open(filename);
data/igor-1.4.0+dfsg/igor_src/Hypermutationglobalerrorrate.cpp:191:27:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	output_Nmer_stat_stream->open(filename);
data/igor-1.4.0+dfsg/igor_src/Pgencounter.cpp:52:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		output_pgen_file_ptr->open(path_to_file + "Pgen_counts.csv");

ANALYSIS SUMMARY:

Hits = 19
Lines analyzed = 20756 in approximately 0.61 seconds (34009 lines/second)
Physical Source Lines of Code (SLOC) = 12459
Hits@level = [0]   0 [1]   0 [2]  11 [3]   0 [4]   8 [5]   0
Hits@level+ = [0+]  19 [1+]  19 [2+]  19 [3+]   8 [4+]   8 [5+]   0
Hits/KSLOC@level+ = [0+] 1.525 [1+] 1.525 [2+] 1.525 [3+] 0.642106 [4+] 0.642106 [5+]   0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.